R help - Jun 2007 - Dissimilarity Analysis

Hello you all!

I am a completely new user of R and I have a problem to solve.
I am using Mac OS X on a PowerBook.

I have a table that looks like this:

            species X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 X14  
X15 X16 X17 X18 X19 X20 X21
1        Anth_cap1  1  0  0  1  0  1  0  0  1   0   0   0   0   0    
0   0   1   0   0   0   1
2       Anth_crin1  1  0  0  1  0  1  0  0  1   0   1   0   0   0    
0   0   0   1   0   0   1
3        Anth_eck1  1  0  0  1  0  1  0  0  1   0   0   0   0   0    
0   0   0   1   0   0   1
4       Anth_gram1  1  0  0  1  0  1  0  0  1  NA  NA  NA  NA   0    
0   0   0   1   0   0   0
5       Anth_insi1  1  0  0  1  0  1  0  0  1   0   0   0   1   0    
0   0   0   1   0   0   1

All columns  are binary coded characters.
The Import was done by this

Test<-read.table("TestRFemMalBivariat1.csv",header = TRUE, sep =
";")

Now I try to perform a similarity analysis with the dsvdis function  
of the labdsv package with the sorensen-Index.

My first question is if all zeros in my table are seen as missing  
values and if it islike that how can I change without turning zero  
into other numbers?

Secondly I tried to perform the analysis as simple as possible, after  
changing the characterstates into 1 and 2 with this code:

  DisTest<-dsvdis(Test, index = "sorensen")

But I always get back this error message:

Warnung in symbol.For("dsvdis") :'symbol.For' is not needed:
please
remove it
Fehler in dsvdis(Test, index = "sorensen") :
	NA/NaN/Inf in externem Funktionsaufruf (arg 1)
Zusätzlich: Warning message:
NAs durch Umwandlung erzeugt

By the way I tried to import my table with the scan function because  
I didn´t really understand what I have to fill in in the what  
Argument if I want to define it as a list.

scan(file = "", what = double(0), nmax = -1, n = -1, sep =
"",
      quote = if(identical(sep, "\n")) "" else
"'\"", dec = ".",
      skip = 0, nlines = 0, na.strings = "NA",
      flush = FALSE, fill = FALSE, strip.white = FALSE,
      quiet = FALSE, blank.lines.skip = TRUE, multi.line = TRUE,
      comment.char = "", allowEscapes = FALSE, encoding =
"unknown")


I hope somedody can help me with my problem and thanks in advance.

Best regards

Birgit

Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
birgit.lemcke@systbot.uzh.ch






	[[alternative HTML version deleted]]

Hi Birgit - looks like you have a few issues here.

Birgit Lemcke <birgit.lemcke <at> systbot.uzh.ch> writes:
> 
> Hello you all!
> 
> I am a completely new user of R and I have a problem to solve.
> I am using Mac OS X on a PowerBook.
> 
> I have a table that looks like this:
> 
>             species X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 X14  
> X15 X16 X17 X18 X19 X20 X21
> 1        Anth_cap1  1  0  0  1  0  1  0  0  1   0   0   0   0   0    
> 0   0   1   0   0   0   1
> 2       Anth_crin1  1  0  0  1  0  1  0  0  1   0   1   0   0   0    
> 0   0   0   1   0   0   1
> 3        Anth_eck1  1  0  0  1  0  1  0  0  1   0   0   0   0   0    
> 0   0   0   1   0   0   1
> 4       Anth_gram1  1  0  0  1  0  1  0  0  1  NA  NA  NA  NA   0    
> 0   0   0   1   0   0   0
> 5       Anth_insi1  1  0  0  1  0  1  0  0  1   0   0   0   1   0    
> 0   0   0   1   0   0   1
> 
> All columns  are binary coded characters.
> The Import was done by this
> 
> Test<-read.table("TestRFemMalBivariat1.csv",header = TRUE, sep
= ";")
First - you need to transpose the matrix to have species as columns.  You can do
this with:

d2 = data.frame(t(Test[,-1]))
colnames(d2) = Test[,1]  #now use d2


 
> Now I try to perform a similarity analysis with the dsvdis function  
> of the labdsv package with the sorensen-Index.
> 
> My first question is if all zeros in my table are seen as missing  
> values and if it islike that how can I change without turning zero  
> into other numbers?
no - the zeros are valid observations.  the na's are missing data.

>   DisTest<-dsvdis(Test, index = "sorensen")
> 
> But I always get back this error message:
> 
> Warnung in symbol.For("dsvdis") :'symbol.For' is not
needed: please
> remove it
> Fehler in dsvdis(Test, index = "sorensen") :
> 	NA/NaN/Inf in externem Funktionsaufruf (arg 1)
> Zus?tzlich: Warning message:
> NAs durch Umwandlung erzeugt


Second - you have an issue with missing data.  It looks like dsvdis does not
like the NA's - so you must make a decision about what to do.  Delete that
species, delete that site, or whatever...

Finally - the warning over symbol.For is an issue with the labdsv library itself
- nothing you are doing wrong.  The results will still be valid - but the use of
symbol.For is something that will eventually need to be changed in the labdsv
library.

hth,

stephen